Bioclipse: an open source workbench for chemo- and bioinformatics

Background  

There is a need for software applications that provide users with a complete and extensible toolkit for chemo- and bioinformatics accessible from a single workbench. Commercial packages are expensive and closed source, hence they do not allow end users to modify algorithms and add custom functionality. Existing open source projects are more focused on providing a framework for integrating existing, separately installed bioinformatics packages, rather than providing user-friendly interfaces. No open source chemoinformatics workbench has previously been published, and no sucessful attempts have been made to integrate chemo- and bioinformatics into a single framework.     

Fast evolutionary genetic differentiation during experimental colonizations

Founder effects during colonization of a novel environment are expected to change the genetic composition of populations, leading to differentiation between the colonizer population and its source population. Another expected outcome is differentiation among populations derived from repeated independent colonizations starting from the same source. We have previously detected significant founder effects affecting rate of laboratory adaptation among Drosophila subobscura laboratory populations derived from the wild. We also showed that during the first generations in the laboratory, considerable genetic differentiation occurs between foundations. The present study deepens that analysis, taking into account the natural sampling hierarchy of six foundations, derived from different locations, different years and from two samples in one of the years. We show that striking stochastic effects occur in the first two generations of laboratory culture, effects that produce immediate differentiation between foundations, independent of the source of origin and despite similarity among all founders. This divergence is probably due to powerful genetic sampling effects during the first few generations of culture in the novel laboratory environment, as a result of a significant drop in N _e. Changes in demography as well as high variance in reproductive success in the novel environment may contribute to the low values of N _e. This study shows that estimates of genetic differentiation between natural populations may be accurate when based on the initial samples collected in the wild, though considerable genetic differentiation may occur in the very first generations of evolution in a new, confined environment. Rapid and significant evolutionary changes can thus occur during the early generations of a founding event, both in the wild and under domestication, effects of interest for both scientific and conservation purposes.     

Oleoyl-Lysophosphatidylcholine Limits Endothelial Nitric Oxide Bioavailability by Induction of Reactive Oxygen Species

Previously we reported modulation of endothelial prostacyclin and interleukin-8 production, cyclooxygenase-2 expression and vasorelaxation by oleoyl- lysophosphatidylcholine (LPC 18:1). In the present study, we examined the impact of this LPC on nitric oxide (NO) bioavailability in vascular endothelial EA.hy926 cells. Basal NO formation in these cells was decreased by LPC 18:1. This was accompanied with a partial disruption of the active endothelial nitric oxide synthase (eNOS)- dimer, leading to eNOS uncoupling and increased formation of reactive oxygen species (ROS). The LPC 18:1-induced ROS formation was attenuated by the superoxide scavenger Tiron, as well as by the pharmacological inhibitors of eNOS, NADPH oxidases, flavin-containing enzymes and superoxide dismutase (SOD). Intracellular ROS-formation was most prominent in mitochondria, less pronounced in cytosol and undetectable in endoplasmic reticulum. Importantly, Tiron completely prevented the LPC 18:1-induced decrease in NO bioavailability in EA.hy926 cells. The importance of the discovered findings for more in vivo like situations was analyzed by organ bath experiments in mouse aortic rings. LPC 18:1 attenuated the acetylcholine-induced, endothelium dependent vasorelaxation and massively decreased NO bioavailability. We conclude that LPC 18:1 induces eNOS uncoupling and unspecific superoxide production. This results in NO scavenging by ROS, a limited endothelial NO bioavailability and impaired vascular function.     

To be an intra‐guild predator or a cannibal: is prey quality decisive?

Abstract.  1. Many cannibalistic species are also intra-guild predators. Such predators will often face the decision whether to consume a conspecific or a heterospecific prey from the same guild. This decision may depend on the relative quality and abundance of the prey but also on other factors such as relatedness by descent, prey-specific defence and the probability of the victim harbouring shared diseases.
2. Here, intra-guild interactions among two cannibalistic species of predatory mites, Iphiseius degenerans and Neoseiulus cucumeris (Acari: Phytoseiidae) that belong to closely related genera were studied.
3. Individuals of I. degenerans were offered a diet of conspecifics or heterospecifics. Because I. degenerans is capable of recognising kin individuals from non-kin, and they were exclusively offered conspecifics that were either distantly related or non-kin, it was expected that it would not refrain from cannibalising for reasons of possible relatedness.
4. When corrected for numbers of victims eaten, survival, and juvenile development of predators fed with intra-guild prey was higher than that of cannibals. This was probably caused by a higher quality of heterospecific victims, even though conspecific victims were larger and therefore potentially contained more food. This led to the prediction that the predators should strongly prefer heterospecific prey. This was indeed borne out in independent choice experiments. Thus, the choice of predators between heterospecific and conspecific prey is not only affected by avoidance of consuming conspecifics, but also by relative prey quality.     

Life mode of in situ Conularia in a Middle Devonian epibole

Abstract: Exceptionally abundant specimens of Conularia aff. desiderata Hall occur in multiple marine obrution deposits, in a single sixth‐order parasequence composed of argillaceous and silty very fine sandstone, in the Otsego Member of the Mount Marion Formation (Middle Devonian, Givetian) in eastern New York State, USA. Associated fossils consist mostly of rhynchonelliform brachiopods but also include bivalve molluscs, orthoconic nautiloids, linguliform brachiopods and gastropods. Many of the brachiopods, bivalve molluscs and conulariids have been buried in situ. Conulariids buried in situ are oriented with their aperture facing obliquely upward and with their long axis inclined at up to 87 degree to bedding. Most specimens are solitary, but some occur in V‐like pairs or in radial clusters consisting of three specimens, with the component specimens being about equally long or (less frequently) substantially different in length. The compacted apical end of Conularia buried in situ generally rests upon argillaceous sandstone. With one possible exception, none of the examined specimens terminates in a schott (apical wall), and internal schotts appear to be absent. The apical ends of specimens in V‐like pairs and radial clusters show no direct evidence of interconnection of their periderms. The apical, middle or apertural region of some inclined specimens abuts or is in close lateral proximity to a recumbent conulariid or to one or more spiriferid brachiopods, some of which have been buried in their original life orientation. The azimuthal bearings of Conularia and nautiloid long axes and the directions in which conulariids open are nonrandom, with conulariids being preferentially aligned between 350 and 50 degree and with their apertural end facing north‐east, and nautiloids being preferentially aligned between 30 and 70 degree. Otsego Member Conularia were erect or semi‐erect, epifaunal or partially infaunal animals, the apical end of which rested upon very fine bottom sediment. The origin of V‐like pairs and radial clusters remains enigmatic, but it is probable that production of schotts was not a regular feature of this animal’s life history. Finally, conulariids and associated fauna were occasionally smothered by distal storm deposits, under the influence of relatively weak bottom currents.     

Transmission of stridulatory signals of the burrower bugs, Scaptocoris castanea and Scaptocoris carvalhoi (Heteroptera: Cydnidae) through the soil and soybean

Abstract.  Males and females of the burrower bug species Scaptocoris castanea Perty and Scaptocoris carvalhoi Becker emit stridulatory signals when on the roots of soybean. The substrate-borne components of the signal can be recorded on the plant but not on the surrounding soil surface. The stridulatory apparatus is composed of the tergal plectrum (lima) and the stridulitrum (stridulatory vein) on the underside of the hind wings. The male plectrum has one ridge and the female lima has 13 ridges. Stridulitra of different species differ in the length and in the number of teeth. Rubbing of plectrum (lima) ridges over the stridulitrum in one or both directions produces pulse trains. The velocity of signals that are recorded less than 0.5 cm from the bug is below 0.013 mm s⁻¹ on the soil and below 0.066 mm s⁻¹ on the leaf surface. Broadband spectra have a dominant frequency of less than 1 kHz and subdominant peaks extending up to 7 kHz. The dominant frequency of the stridulatory signal transmitted through a plant decreases together with the proportion of its higher frequency spectral components. Signals are attenuated for 3–9 dB cm⁻¹ when transmitted through the soil or soybean leaf and for approximately 1 dB cm⁻¹ when transmitted through soybean stem.     

Kinome-wide interaction modelling using alignment-based and alignment-independent approaches for kinase description and linear and non-linear data analysis techniques

Background  

Protein kinases play crucial roles in cell growth, differentiation, and apoptosis. Abnormal function of protein kinases can lead to many serious diseases, such as cancer. Kinase inhibitors have potential for treatment of these diseases. However, current inhibitors interact with a broad variety of kinases and interfere with multiple vital cellular processes, which causes toxic effects. Bioinformatics approaches that can predict inhibitor-kinase interactions from the chemical properties of the inhibitors and the kinase macromolecules might aid in design of more selective therapeutic agents, that show better efficacy and lower toxicity.     

Mass ivermectin treatment for Onchocerciasis: Lack of evidence for collateral impact on transmission of Wuchereria bancrofti in areas of co-endemicity

There has long been interest in determining if mass ivermectin administration for onchocerciasis has 'unknowingly' interrupted lymphatic filariasis (LF) transmission where the endemicity of the two diseases' overlaps. We studied 11 communities in central Nigeria entomologically for LF by performing mosquito dissections on Anopheline LF vectors. Six of the communities studied were located within an onchocerciasis treatment zone, and five were located outside of that zone. Communities inside the treatment zone had been offered ivermectin treatment for two-five years, with a mean coverage of 81% of the eligible population (range 58–95%). We found 4.9% of mosquitoes were infected with any larval stage of W. bancrofti in the head or thorax in 362 dissections in the untreated villages compared to 4.7% infected in 549 dissections in the ivermectin treated villages (Mantel-Haenszel ChiSquare 0.02, P = 0.9). We concluded that ivermectin annual therapy for onchocerciasis has not interrupted transmission of Wuchereria bancrofti (the causative agent of LF in Nigeria).